Summer Homework 6: A Question For Slartibartfast

Imagine you could ask Slartibartfast (look him up!) any question about the Earth. What would you ask him, and why?

This prompt was a bit of a leftfield task for my students. Many of them have never read/listened to/watched The Hitchhiker's Guide to the Galaxy. I, on the other hand, apparently made my entrance into this world while my father repeatedly read the first chapter of the book out loud, and the radio series was the soundtrack to many long car journeys.

When I got to Cambridge University, it turned out that one of my lecturers, Simon Conway Morris, was rather a big fan of the book too. His lecture notes were peppered with references to 42, "life, the universe and everything", and in particular the character Slartibartfast. Slartibartfast designed planets - he designed Earth, and after the Vogons blew up Earth #1, he was in the process of designing Earth #2. This prompt is a paraphrase of a genuine Part III long essay exam question we sat. Buggered if I can remember what I asked him - it was a decade ago - but this is what I'd ask this time.

When you make a new planet, do you have to start life off from scratch, or can you copy and paste it in from another planet?
I've already mentioned in the previous post my interest in abiogenesis. If life arises independently on each planet, then the conditions must have been optimum for the synthesis of more complex organic molecules on the Earth at the time. If it is possible for organisms or complex organics to be transported through space, then the conditions under which life originated could be very different to those experienced during Earth history. The hypothesis that living organisms had extraterrestrial origins (and we're talking single-celled organisms or even nucleic acids here, not ET phoning home) is called Panspermia - most of my students will only have heard of it in the context of the film "Prometheus" - the film is not a scientific account of this hypothesis...

What made you decide to go for carbon, hydrogen, nitrogen and oxygen as such fundamental elements? Why not silicon, lithium, boron and fluorine?
Life as we know it requires water. All metabolic reactions occur in an aqueous environment, and I should think (though I am not a great biochemist) that such a demand places certain constraints on the molecules involved in these reactions. But I'd be interested to know if this is the only option. I remember the odd "Star Trek" episode involving silicon-based life-forms - no jokes about Katie Price, these were invariably sentient rocks (oh okay then, you can make a joke about Katie Price).

Seriously, what was wrong with dinosaurs? Why did you kill them off and leave their bones in the ground as tantalising glimpses of our prehistory?
Just because, damnit, I think they're awesome. I'd like to understand exactly what was going on environmentally at the end of the Cretaceous, and to be able to see why non-avian dinosaurs and many other taxa were unable to cope with these conditions. Palaeontologists have a jolly good idea about this, but it would be nice to understand what made dinosaurs so successful, and why they could not weather the bolide impact.

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Summer Homework 5: An Exciting Discovery

What, for you, has been the most exciting scientific discovery of the past decade? How has it influenced your life or your studies? Why do you consider it to be so exciting?

In 1996, before I began my A-levels, I was set some summer homework, to collect relevant biology-related news articles. This was in the days before readily available internet, and so I had to read newspapers. Just under a month before I started sixth form, the world went crazy over Martian microbes.


SEM image of "microbe" structures in meteorite ALH84001, from NASA
Later, while on my ill-fated attempt at a PhD at Washington University in St Louis, fellow students and their professors were involved with the Mars Exploration Rovers. Our Head of Department was the deputy science PI. We were all herded into the large lecture theatre one Thursday afternoon to watch NASA's "30 Seconds To Mars" video of the landings (though it didn't have this soundtrack):


The objectives for the mission were largely geological and hydrogeological - confirming the existence of water on Mars. Spirit and Opportunity did not disappoint. Within a couple of months of landing, Opportunity identified minerals indicative of a watery past - minerals such as haematite and jarosite form in the presence of water. Not only that, jarosite forms in acidic water, similar to that found in Spain's Rio Tinto, which provides an analogue for the environment in that area of Mars. Spirit found goethite, which only forms in the presence of water.

Four years later, the Phoenix lander found ice at the poles. Over the past decade rocks have also been found with cross-bedding and other features, indicating liquid water existed on Mars at some point.

In the early hours of Monday 6th August, the Curiosity rover landed on the surface of Mars, bringing with it the Mars Science Laboratory. The aim of the mission is to identify organic molecules, or at least trace molecules indicating that organics existed on the surface of Mars. This would provide evidence for life on Mars at some point in its history.

Why am I, a palaeontologist-turned-biology-teacher, so interested in the evidence for liquid water on Mars? One of the most frustrating misconceptions I come across is the erroneous idea that biologists are trying to use evolution to explain the appearance of life on Earth. In fact, evolution does nothing to explain origins of life - this is all down to abiogenesis. By studying what might have happened on Mars, we have the opportunity to look back in time. We know a fair bit already about how molecules can join together in increasing complexity, and we know a bit about early archaean organisms. But in Mars we may have a "stopped clock" of early life in the Solar System.


In short, if we can figure out why there is no complex life form on Mars, then we can figure out why there is complex life on Earth. It goes deeper than just being a "Goldilocks planet". In answering questions about our neighbouring planets, we may find the answers to the questions we're asking about ourselves.

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Summer Homework 4: Saving The World

Is there any point trying to save the Earth? Describe arguments for and against environmentalism, and offer your conclusions on the fate of the human race.

The Earth has been through some interesting times in its 4.54Ga history. There is evidence that it was covered in ice at various points (though the extent of this ice is somewhat debated still), and that there were times when it was a really crap place to live, such as the Paleocene-Eocene Thermal Maximum. Life on Earth has been through a number of mass extinctions, most notably the Permian-Triassic extinction, resulting in the obliteration of 90% of marine species.


Marine extinction intensity, from Wikipedia
Species have appeared and disappeared. More than 99% of all species that have ever existed on the Earth are extinct. Big deal.

The climate has changed - though we are talking about global warming, we are in a much colder period now than many periods in the past. It has been both warmer and colder than this in the Phanerozoic eon alone. So who's to say that this hasn't all happened before? In fact, the idea of a "resilient Earth" is used frequently as an argument against anthropogenic global warming.


Phanerozoic climate change, from Wikipedia
And yet this is not a comforting state of mind to have. Species go extinct, climate changes, all over geological time scales - that is, over millions of years. Historically, climate has changed sufficiently slowly as to enable species to migrate or facilitate adaptation and evolution. Local changes may be rapid, but global changes are slower (notwithstanding bolides, large-scale volcanism, and so on). What's happening at the moment is faster than we've seen before.


Hockey stick curve, from IPCC 3rd Annual Report
Now, it is possible that we are seeing this rapid change because we are able to see our recent fossil record with greater resolution than the more distant past. However, since the start of the Industrial Revolution, we have burnt millions of years' worth of fossil fuels, chucking tonnes of carbon dioxide back into the atmosphere over and above the normal flux of the carbon cycle. There is a causal mechanism linking atmospheric carbon dioxide levels to global temperatures, via the greenhouse effect. We have lost the golden toad, the Yangtze river dolphin, the Pyrenean ibex, the Western black rhino and the Pinta Island tortoise, just in the past decade or so, and that's just the cute cuddly vertebrates - Flying Spaghetti Monster only knows how many invertebrates and plants have become extinct in that time (though my guess would be hundreds).

As these organisms die out, they clearly affect the ecosystems to which they belong. And of course, Homo sapiens is part of these ecosystems. A soundbite often attributed to Albert Einstein says we'd have about four years left if the honey bees became extinct. It may be hyperbole, but it's rooted in a truth - we depend on the pollination of plants, whether it is by insect or wind. Extinction of many of these species will have a disastrous effect on our survival.

Climate, too, will affect us. We are seeing more droughts, more storms and more extreme weather. As the average annual temperature increases, the arid and semi-arid biomes spread towards the poles. We can grow Mediterranean crops in the southern UK. The boundaries of our major ecosystems are pushing polewards, leaving plants and animals stranded, unable to migrate or colonise quickly enough.

In the end, the Earth probably will recover. The ferns, the cockroaches and the lawyers will survive the next great extinction. The populations of other organisms will bottleneck, and there will be increased diversity millions of years later. But humans are unlikely to make it.


We need to save the Earth and its residents. Without the bacteria, fungi, plants and other animals, we are doomed. The Earth is the only home we have ever known, and if we break it we're not getting another.

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Summer Homework 3: Ecological Fieldwork

Summarise the ecological practical work you carried out on campus. Describe the factors affecting the distribution of the organism studied. Apply what you have learned about competition, niches and abiotic factors to this distribution.

Loathing, as I do, the desire to have a monoculture of grass, I'm quite happy to see other plants in my lawn. In particular, I love how soft the moss feels when I walk barefoot on it. The moss concerned is Rhytidiadelphus squarrosus, the springy turf-moss, and it is the most common moss found in lawns in the UK. It's pretty ubiquitous, and adapted to a wide range of soil types, though all mosses depend on moist conditions.


Fig. 1: The garden, looking south to the widest part of the garden.
The garden is trapezium-shaped, and this section of turf is 18m long and 6m wide at the narrowest point. There are four trees in the garden. The three between 13m and 15m from the left hand side have, in the past, left the soil underneath very dry, killing some of the grass.


Fig. 2: Cartoon map of area of garden used in study.
I set three belt transects, 18m by 0.5m, using a 0.25m² quadrat and a tape measure. The transects were 1m apart. I systematically sampled every 1m along the transect, estimating the percentage cover of moss, and measuring the pH and moisture content of the soil at 5cm depth.


Fig. 3: Average percentage cover of moss against distance from wall
There is a clear decline at 12m, coinciding with the proximity to the three large trees in the garden. However, there is no clear change in either pH or moisture in this area. I would add that we are currently having the wettest summer I can remember, and that a more accurate idea of soil moisture or precipitation would require long-term monitoring rather than shoving a cheap meter in the soil at regular intervals.

There is also no correlation between the percentage cover of moss and either pH or moisture.

   
Fig. 4: No correlation between pH or moisture and percentage cover of moss.
Spearman's rank correlation coefficients for these pairs of data are -0.1238 and -0.0483 respectively, which supports my assertion of no correlation. It is possible that biotic factors such as competition for resources from the other plants, namely the three large trees (two maples, Acer pseudoplatanus, and a half-dead, woodworm-infested excuse for an ash), are responsible. Whether it is an undetected competition for water, or perhaps minerals, I cannot tell. The grass, clover and other plants seem to be the opportunists, just finding space to grow where the moss cannot, rather than the other way round.

In the end, though, I suspect that soil moisture is responsible. I did not look at the water levels at shallower depths, which may have reflected the availability of water for the moss more accurately. Nor did I consider the long-term trends in the garden in terms of soil moisture. The investigation could be enhanced with the longer-term monitoring of water levels, perhaps considering the sunlight (though the areas with highest moss distribution are the sunniest, by my observations!), and maybe investigating the macro- and micro-nutrient content of the soil. I'd be very happy to remove all the grass from the area too, to see if the grass was outcompeting the moss, contrary to my suggestion.

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(Note, students: I don't expect anything more than this. I don't even really expect much in the way of statistics, just that you have considered the ecology of the area you have studied.)

Summer Homework 2: Science Communication

Research the ways in which scientists can communicate with other scientists and with the general public. What are the advantages and disadvantages of each method? What are the benefits and drawbacks of the existing peer-review method for academic publications? How do you feel peer-review could be improved?

Several methods of communication exist for scientists to educate others about their research. They range from the formal (journal articles), to semi-formal (conferences), to informal (newspapers, television shows, outreach programmes).

Journal articles and edited books
In general, when scientists wish to communicate their research formally to other scientists in the field, they need to subject their work to peer-review, where other scientists in the field read the work, try to replicate the results and give (hopefully) formative feedback that will improve the quality of the research. Scientific journals are considered the best way of achieving that. Scientists are assessed, especially if they work in universities, on the length and prestige of their publication record. With a few exceptions, it seems the shorter the journal title, the more prestigious it is, e.g. Science, Nature, Cell. The advantages are, no doubt, the prestige, the rubber-stamp of authority from the peer-review process, and the knowledge that the important researchers in your field will see your work. The disadvantages are the length of time it takes from submission to publication (18 months is not unusual), and the cost of accessing the articles for people who do not have an institutional subscription to the journal.

Conferences
When scientists have work in progress, a conference can be a good place to present this, prior to publication. Abstracts (short summaries) are submitted, and subjected to a mild form of peer-review (i.e. the committee decides whether the abstract sucks or not). They are then published in a conference volume. The conference takes place, and the scientists present their work either as a talk, usually between 10-20 minutes long, or as a poster in a 2-3 hour poster session.


The advantages of this are the ability to talk to scientists in related fields, get ideas, swap knowledge of specimens/techniques, and to showcase one's own talents. It's an opportunity to collaborate with others. The disadvantages are the cost of travel and accommodation, and difficulties with getting time out of teaching or other commitments. Often, the conference organisers will have a press conference, which can raise a problem of a specimen being reported in the press that has not been officially named or published in a journal. This can be awkward for all involved.

Press releases to newspapers
If a piece of work is considered worthy, then the institution or journal may write a press release. This is sent to journalists in advance of the release of the article, so they are able to research and write their own piece. Sometimes this can result in an unfortunate game of Chinese Whispers - the press release doesn't quite get the science correct, and the news report doesn't quite interpret the press release correctly, and a scientist may find, say, that they've been quoted as saying that there are only 500 dinosaur species left to be discovered (!). However, this is probably the most common means of getting information to the general public, through the popular press. And there have been some really interesting cases that have arisen from press releases and press conferences.

Blogging and outreach
With some of the issues related to press releases, many scientists have decided to cut out the middle men (the press officers and journalists) and communicate directly with the public. Science blogging is becoming more and more popular, with big organisations such as Scientific American, Wired and Discover Magazine getting in on the action. The advantages are that the scientists get to tell the public exactly what they want to say, and the public get to ask the scientists questions directly. However, the disadvantages are that, while there are many journalists that slip up on the science, there are many scientists that really don't have the communication skills to make their science sound interesting. Plus, any old nutjob can set up a blog...

Where next?
Peer-review is a pretty decent method, all told. It gives credibility to the research and shows that other scientists have deemed the methods to be accurate and the data to be genuine. Publication in a scientific journal is a chartermark of sorts. However, it is not foolproof - there have been examples where peer-review has not caught academic fraud. I'd like to see double-blind peer-review as standard - the authors don't know who the reviewers are, and the reviewers don't know who the authors are, until publication. There is evidence that this improves the representation of female first authors, so presumably removing inherent sexism and prejudice that female authors can't do science...

Journal articles are also prohibitively expensive - it can be $35 to access a short communication in a journal, rendering much research inaccessible to people who are not at a wealthy university with an institutional subscription. However, there are moves towards open access for all government-funded research (surely only fair?), and there are pretty high-impact open access journals such as PLoS, who are giving the big academic publishers a run for their money. I would like to see more online free publication of scientific journal articles, each with the means to comment on them and debate the implications of the results or conclusions. That would be awesome.

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Summer Homework 1: My Life In Science

Introduce yourself (to the extent that you are willing to be identified). Write about your earliest memories of science. How have these influenced you to study the sciences? Do you wish to continue to study sciences at university? If so, what made you choose this subject? If not, what has captured your mind more than science?

I am Julia Anderson, biology lecturer. I used to be Julia Heathcote, palaeontologist.

I was fortunate, growing up, to have parents who were pretty progressive in terms of gender stereotypes. I had as many trucks as dolls, a Fisher Price tool kit and doctor's kit. I pretty much lived in dungarees as a baby and toddler.


I was already perfecting That Look, though I think my hair looks better now.
Dad had cause to visit London at weekends, and would often stop off at the Natural History Museum when it was free for the last half hour or so. And he bought me a plastic dinosaur. It was a dark maroon injection-moulded Tyrannosaurus. This was swiftly followed by a beige Triceratops, yellow Iguanodon and green Megalosaurus. I was hooked.

From then on it was all about the science, and even more so, it was about the dinosaurs. My junior school teacher was impressed that, at the age of nine, I could spell the word "palaeontologist". My dad was convinced I was going to be his "Ellie", and that I would be a great scientist. There was a whole-family outing to see "Jurassic Park" when it came out in the cinema. On our first and only holiday as a family to the USA we went round an obscene number of museums. They endured afternoons fossil-hunting on beaches in Scotland and Dorset while on holiday.

I was academically excellent, so I won a scholarship to Nottingham High School for Girls for the sixth form. It was the only way I could do four A-levels (how times have changed!). I applied to, and was offered a place at Gonville & Caius College, the same Cambridge college my father had attended. I got the three A grades I needed, and spent a moderately miserable four years at university, before doing a Masters and being offered a PhD place in the US. That didn't work out so well, and I returned to the UK. I spent five years drifting from admin job to admin job, before taking a leap of faith and figuring I may as well become a teacher.

I was fascinated by the unknown, the other worlds that had existed on the Earth, completely unrecognisable. Dinosaurs and other large, mostly extinct taxa, have captured the minds of people in this way for centuries. I was particularly enamoured of sauropods, the ones with the long necks and tails. The evolution of gigantic forms was fascinating. Nothing like them has existed since. What was it about the Earth's environment that enabled this size increase? I remember a common put-down from my PhD supervisor being "You're not curing cancer". No, but sometimes knowledge for knowledge's sake makes human beings better people. Sometimes understanding the past can help us avoid disastrous conditions in the future. Those who do not learn from history are doomed to repeat it.

But in the end it wasn't for me. I tried to combine teaching with a reboot of my PhD part-time, but couldn't combine the two successfully. In the end, my students won. I have never regretted this decision. I get to work with clever, funny, curious, irreverent, kind youngsters every day. I get to help them see what a wonderful and awesome universe we live in. I get to raise their aspirations and create the scientists of the next decade.

I will never lose my curiosity and enthusiasm for science. I love to read up on new discoveries and breakthroughs, and I love to share that with my students. I will never be Dr Julia Heathcote, but as Mrs Julia Anderson I get to be Miss, Jules, Mum (!) and Prof - all genuinely things I've been called by students. And one day, maybe, a student who has been inspired to study life sciences at university by me and my teaching, whether it's an A-level, BTEC or HND student, might cure cancer.

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Summer Homework: Doing It Myself

A few weeks ago, I set summer homework for my little darlings. Some of the posts have been brilliant, and all have been enjoyable to read.

However, there are a lot of students who haven't yet made their blogs, let alone started posting. One of my girls has said I'll find all the posts appearing on 15th August, the day before the deadline. This is possible, but it's more likely that I won't see any work at all from any of the students.

There will be a number of complaints, such as it being too difficult, or them not having enough time, and so on. So I'm going to show them (though unless the AS students have found my blog already they won't see it until after the deadline) that the work can easily be done.

Not only that, I'm going to write all six posts, including a practical writeup of a quadrat-chucking exercise. I'm going to borrow a quadrat from the College and analyse the biodiversity of my back garden. This will hopefully take account of the advantage I have of being a more experienced writer.

I'll be posting these regularly over the next month, and when I do, I'll try to remember to update this post to include links to all of the individual articles. I'll even shove in a word count so they can see I'm doing about 400-600 words just like them.

Summer Homework #1: My Life In Science
Summer Homework #2: Science Communication
Summer Homework #3: Ecological Fieldwork
Summer Homework #4: Saving The World
Summer Homework #5: An Exciting Discovery
Summer Homework #6: A Question For Slartibartfast